Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

9.3 PLATON - ANALYSE Menu

 

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Chapter. 9.3  PLATON

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7.2 N

ONSTANDARD SETTINGS WITH CELL TRANSFORMATIONS

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8. ATOMIC RADII USED IN PLATON .......................................................................................................... 30

9.  INTERNAL PARAMETERS........................................................................................................................ 30

10. CIF-VALIDATION DOCUMENTATION (VALIDATION.DOC) ......................................................... 30

11. SQUEEZE, AN EFFECTIVE CURE FOR THE DISORDERED SOLVENT SYNDROME IN

CRYSTAL STRUCTURE REFINEMENT...................................................................................................... 41

11.1 G

ENERAL

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11.2 I

MPLEMENTATION AND 

U

SE

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11.3 N

OTES ON 

SQUEEZE ............................................................................................................................... 42

11.4 I

NTERPRETATION OF THE RESULTS

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12  PLATON IN THE WINGX IMPLEMENTATION.................................................................................... 43

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9.3 PLATON - ANALYSE Menu

 

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Chapter. 9.3  PLATON

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1. Introduction to PLATON

Platon is a general crystallographic tool implementing:

•  a large variety of standard geometrical calculations, i.e. bonds, angles,   torsions, planes,

rings, inter-molecular contacts (H-Bond analysis), co-ordination etc,  either fully automatic

or as specified

•  tests:  e.g. ADDSYM (based on Yvon LePage's powerful published MISSYM (C)

algorithm), VOIDS etc.

•  utilities: cell transformation, SHELXL input etc., PDB & CIF output

•  graphics: e.g. automatic labelled 'ORTEP-lookalike plots, the molecular graphics program

PLUTON and NEWMAN plots, inspection for completeness of the dataset with ASYM-

VIEW

•  several filters: e.g. exact analytical/de Meulenaer & Tompa face-indexed correction for

absorption, DELABS (the locally modified Walker & Stuart DIFABS technique for

empirical absorption correction), psi-scan based on with MULABS using multiple scanned

reflections (following the Blessing algorithm) and SQUEEZE for handling disordered

solvents.

•  validation checks for data supplied in CIF-Format, implementing most published tests

done in Chester on papers submitted for publication in Acta Cryst + a large number of

'PLATON-related' tests

Most PLATON features complement those available in the widely distributed public domain

SHELX97 package.

NOTE  Most features are currently available only for non-protein structures.

1.1 Coordinate data input standards 

Parameter data may be given in various formats including CSD-FDAT, CIF, PDB & SHELX

.RES standards. There are some restrictions on atom labelling (A4). A CIF file is

recommended when su's (= e.s.d.'s) on the derived geometry parameters are desired.

1.2 Reflection data format

Reflection data should be provided in the SHELX format (optionally with SHELX76-style

direction cosines. Some program options also accept SHELXL97-style FCF CIF's as

reflection input.

1.3 Menus and mouse clicking

PLATON automatically opens a Window Menu. In the menu mode, input can be given either

from the keyboard (useful for the more complex instructions) or via mouse clicks.

The Window  Menu area is divided in four sub-windows. 

1.  The main graphics area in the upper-left corner (also used for the main PLATON

(opening) menu from which various (sub)programs can be started  by mouse clicks).

2.  The upper-right window carries varies sup-menus with clickable options. Currently active

options are displayed in RED. Entries in this menu with vertical lines indicate click-

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9.3 PLATON - ANALYSE Menu

 

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position sensitive options or magnitudes.  The yellow top-field may be clicked to refresh

the window contents.

3.  The lower-Left window is used for short messages and the display of  keyboard input.

4.  The lower-right window informs about the current input status. It also provides an easy

'Exit' by clicking on it.

More extensive output is produced on the window from which the program was started and on

the listing file.

1.4 Introductory tutorial

A sample run of the program using  the test data in 'sucrose.spf' is executed by the interactive

instructions (on the program prompt >>):

>> CALC (or click on 'CALC ALL')

This will give an exhaustive geometry analysis. The main results are on the listing file to be

printed on an ASCII lineprinter. Some summary information is also directed to the display.

Alternatively, after restarting the program, the instruction :

>> CALC ADDSYM 

will provide a test for missed symmetry (cf. the LePage MISSYM (C) algorithm),  or:

>> CALC SOLV 

will do a calculation to identify missed solvent areas or

>> TABL ACC

will generate a file as a starting point of a CIF-file suitable for submission to Acta Cryst C.

A default labelled ORTEP is produced with:

>> PLOT ADP

The SQUEEZE option  is executed with:

>> CALC SQUEEZE

A file named name.HKP contains a new reflection file where the disordered solvent

contribution is subtracted from the observed data. Further refinement can be done against this

new file. See Section 10 below for further details.

A similar filter may be set-up to do a DIFABS-type of absorption correction.

>> CALC DELABS

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